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- PDB-4d8l: Crystal structure of the 2-pyrone-4,6-dicarboxylic acid hydrolase... -

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Basic information

Entry
Database: PDB / ID: 4d8l
TitleCrystal structure of the 2-pyrone-4,6-dicarboxylic acid hydrolase from sphingomonas paucimobilis
Components2-pyrone-4,6-dicarbaxylate hydrolase
KeywordsHYDROLASE / STRUCTURAL GENOMICS / PROTEIN STRUCTURE INITIATIVE / NEW YORK STRUCTURAL GENOMIX RESEARCH CONSORTIUM / NYSGXRC / PSI-2 / New York SGX Research Center for Structural Genomics
Function / homology
Function and homology information


2-pyrone-4,6-dicarboxylate lactonase / 2-pyrone-4,6-dicarboxylate lactonase activity / 3,4-dihydroxybenzoate catabolic process / lignin catabolic process
Similarity search - Function
Amidohydrolase / Amidohydrolase-related / Metal-dependent hydrolases / Metal-dependent hydrolase / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
2-pyrone-4,6-dicarboxylate hydrolase
Similarity search - Component
Biological speciesSphingomonas paucimobilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsMalashkevich, V.N. / Toro, R. / Bonanno, J. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: Biochemistry / Year: 2012
Title: Structure and Catalytic Mechanism of LigI: Insight into the Amidohydrolase Enzymes of cog3618 and Lignin Degradation.
Authors: Hobbs, M.E. / Malashkevich, V. / Williams, H.J. / Xu, C. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / Raushel, F.M.
History
DepositionJan 10, 2012Deposition site: RCSB / Processing site: RCSB
SupersessionJan 25, 2012ID: 2QAH
Revision 1.0Jan 25, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2012Group: Structure summary
Revision 1.2Oct 3, 2012Group: Database references
Revision 1.3Jan 9, 2013Group: Database references
Revision 1.4Jan 23, 2013Group: Database references
Revision 1.5Feb 20, 2013Group: Database references
Revision 1.6Nov 21, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.7Feb 10, 2021Group: Database references / Structure summary
Category: audit_author / citation_author / struct_ref_seq_dif
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_ref_seq_dif.details
Revision 1.8Feb 28, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 2-pyrone-4,6-dicarbaxylate hydrolase


Theoretical massNumber of molelcules
Total (without water)34,0311
Polymers34,0311
Non-polymers00
Water4,234235
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.100, 73.170, 82.750
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Detailsmonomer

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Components

#1: Protein 2-pyrone-4,6-dicarbaxylate hydrolase / 2-pyrone-4 / 6-dicarboxylic acid hydrolase


Mass: 34030.770 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sphingomonas paucimobilis (bacteria) / Strain: SYK-6 / Gene: ligI, SLG_12570 / Plasmid: BC-PSGX3(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: O87170, 2-pyrone-4,6-dicarboxylate lactonase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 235 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.32 Å3/Da / Density % sol: 46.92 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 30% PEG 4000, 0.1M TRIS-HCL PH 8.5,0.2 MG CHLORIDE, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 27, 2007
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionRedundancy: 1.8 % / Av σ(I) over netI: 16.69 / Number: 61399 / Rmerge(I) obs: 0.057 / Χ2: 1.61 / D res high: 2 Å / D res low: 50 Å / Num. obs: 35073 / % possible obs: 84.2
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.315088.310.0342.921.7
3.424.3190.410.0433.1911.7
2.993.4291.810.0592.4481.7
2.712.9992.410.0761.8961.7
2.522.719310.0991.4271.7
2.372.5289.910.1191.0021.7
2.252.3784.710.1550.8691.8
2.152.2578.110.1840.7231.8
2.072.1571.410.2380.6371.8
22.0761.810.2730.5841.8
ReflectionResolution: 2→50 Å / Num. obs: 35073 / % possible obs: 84.2 % / Redundancy: 1.8 % / Rmerge(I) obs: 0.057 / Χ2: 1.608 / Net I/σ(I): 11.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2-2.071.80.27325400.584161.8
2.07-2.151.80.23829930.637171.4
2.15-2.251.80.18432540.723178.1
2.25-2.371.80.15535520.869184.7
2.37-2.521.70.11937301.002189.9
2.52-2.711.70.09938771.427193
2.71-2.991.70.07638411.896192.4
2.99-3.421.70.05938192.448191.8
3.42-4.311.70.04337823.191190.4
4.31-501.70.03436852.92188.3

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
SHELXphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
CBASSdata collection
HKL-2000data reduction
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 2→19.91 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.927 / WRfactor Rfree: 0.21 / WRfactor Rwork: 0.1576 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8348 / SU B: 8.297 / SU ML: 0.123 / SU R Cruickshank DPI: 0.2489 / SU Rfree: 0.2015 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.249 / ESU R Free: 0.202 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2288 863 5.1 %RANDOM
Rwork0.1715 ---
obs0.1743 17021 77.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 84.76 Å2 / Biso mean: 33.881 Å2 / Biso min: 12.96 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 2→19.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2316 0 0 235 2551
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0192386
X-RAY DIFFRACTIONr_angle_refined_deg1.3191.9623255
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7425293
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.33123.158114
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.38415368
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.51522
X-RAY DIFFRACTIONr_chiral_restr0.0860.2343
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0221889
LS refinement shellResolution: 2.002→2.054 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.166 15 -
Rwork0.225 247 -
all-262 -
obs--17.37 %
Refinement TLS params.Method: refined / Origin x: 40.7749 Å / Origin y: 39.4309 Å / Origin z: 9.6797 Å
111213212223313233
T0.0186 Å2-0.0055 Å2-0.0051 Å2-0.0271 Å20.0393 Å2--0.0753 Å2
L1.3065 °2-0.1499 °20.1178 °2-1.1617 °2-0.262 °2--0.6512 °2
S0.0153 Å °-0.1357 Å °-0.3029 Å °0.0462 Å °-0.013 Å °0.0209 Å °0.0079 Å °0.0084 Å °-0.0023 Å °

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